iMODFIT intro
iMODFIT is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in Internal Coordinates. Please, download the 2019 version: v1.51.
Flexible fitting in internal coordinates with a reduced number of normal modes provides a natural way to alleviate overfitting distortions, such as poor resolution, map defects (e.g., scale inaccuracies, missing densities, resolution anisotropy), or even partial correspondence between the map and the atomic structure.
iMODFIT has been used by different groups to obtain impressive flexible fittings of:
Yeast Golgi AP-3 complex (Schoppe et al., J. Biol. Chem. 2021)
Papillomavirus E1 helicase replication fork (Javed et al., Nat. Commun. 2021)
Human Integrin αIIbβ3 receptor (Sorrentino et al., PNAS 2021)
Human GluN2A and GluN2B NMDA receptors (Tian et al., Nat. Commun. 2021)
Human Alpha2-macroglobulin (Jourdi et al., Int. J. Biol. Macromol. 2021)
Vibrio cholerae DnaB helicase (molecular replacement) (Marsin et al., Nucleic Acids Res. 2021)
Vegetable Hsp21-DXPS complex (Yu et al., Nat. Commun. 2021)
Human PRC2-activating cofactors JARID2 and AEBP2 (Kasinath et al., Science 2021, see Supplementary)
Porcine Cardiac Actomyosin Complex (Risi et al., Structure 2021)
Human tyrosine hydroxylase (Valpuesta et al., Europe PMC 2020)
SARS-CoV-2 Spike prefusion structures (Melero et al., IUCrJ 2020)
Coxsackievirus B-3 virus-like particles (Hankaniemi et al., Microorganisms 2020)
Chicken Focal Adhesion Kinase (Acebrón et al., EMBO J. 2020)
Asymmetric anthrax lethal toxin (Antoni et al., PLoS Pathog. 2020)
Shigella type III needle complex (Lunelli et al., PLoS Pathog. 2020)
Human ID2 complex on DNA (Rennie et al., EMBO Rep. 2020)
Prokaryotic LdcI–RavA cage-like complex (Jessop et al., Communications Biology 2020)
Murine Perforin-2 (Ni et al., Science Advances 2020)
Human BBSome (Klink et al., Elife 2020)
Capsids from bacteriophage SPP1 (Ignatiou et al., Nat. Commun. 2019)
Lysine decarboxylase (LdcA) from P.aeruginosa (Kandiah et al., Structure 2019)
TcA toxins components (Leidreiter et al., Science Advances 2019)
Yeast Remodeling the Structure of Chromatin complex (Patel et al., eLife 2019, see Supplementary)
Human dynein-2 complex (Toropova et al., Nat. Struct. Mol. Biol. 2019)
Human mLST8–CCT complex (Cuéllar et al., Nat. Commun. 2019)
Tc holotoxin (et al., PNAS 2019)
Prokaryotic aminopeptidase TET2 (Gauto et al., Nat. Commun. 2019)
Prokaryotic potassium channel MloK1 (Righetto et al., Nat. Commun. 2019)
Murine NMDA receptor ( et al., 2018)
Human Membrane Attack Complex (Menny et al., Nat. Commun. 2018)
α-Xenorhabdolysin pore-forming toxin (Schubert et al., eLife 2018)
Human nicotinic acetylcholine receptor α7 (Newcombe et al., Mol. Pharmacol. 2018)
Human PRC2-dinucleosome (Poepsel et al., Nat. Struct. Mol. Biol. 2018)
Human PRC2 (Kasinath et al., Science 2018)
Human Robo1 ectodomain (Aleksandrova et al., Structure 2018)
AAA+ chaperone ClpC from E.coli (Carroni et al., eLife 2017)
NAIP5/NLRC4 murine inflammasome (Tenthorey et al., Science 2017)
Actin 1 filament from malaria parasite (Pospich et al., PNAS 2017)
Mitotic kinesin MKLP2 (Atherton et al., eLife 2017)
Hsp100 disaggregase from E.coli (ClpB) (Deville et al., Science Advances 2017)
Yeast R2TP complex (Rivera-Calzada et al., Structure 2017)
Human parechovirus 3 (Shakeel et al., Nat. Commun. 2016)
TcdA1 toxin (Gatsogiannis et al., Nat. Struct. Mol. Biol 2016)
Yeast RNA polymerase I (Pilsl et al., Nat. Commun. 2016)
PRC1-microtubule complex (Kellogg et al., PNAS 2016)
Human p53/RNA polymerase II complex (Singh et al., Genes & Dev. 2016)
Human cytoplasmic actomyosin complex (Von der Ecken et al., Nature 2016)
Human TFIID (Lauder et al., Nature 2016)
RavA ATPase (Kandiah et al., Sci Rep. 2016)
DnaKNBD-GrpE complex ( Melero et al., JBC. 2015)
Human parechovirus 1 (Shakeel et al., J. Virol. 2015)
Mature HIV-1 capsid (Zhao et al., Nature. 2013, see Supplementary)
Human coxsackievirus (enterovirus) (Shakeel et al., J. Virol. 2013)
ATP synthase from T.thermophilus (Lau and Rubinstein, Nature 2012)
Yeast vacuolar ATPase (Oot et al., Structure 2012)
References
iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates (2013). López-Blanco J.R. and Chacón P. JSB 184(2):261–270
